scholarly journals The complete mitochondrial genome of Dysgonia stuposa (Lepidoptera: Erebidae) and phylogenetic relationships within Noctuoidea

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8780
Author(s):  
Yuxuan Sun ◽  
Yeshu Zhu ◽  
Chen Chen ◽  
Qunshan Zhu ◽  
Qianqian Zhu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Intergenic Spacer ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Rna Genes

To determine the Dysgonia stuposa mitochondrial genome (mitogenome) structure and to clarify its phylogenetic position, the entire mitogenome of D. stuposa was sequenced and annotated. The D. stuposa mitogenome is 15,721 bp in size and contains 37 genes (protein-coding genes, transfer RNA genes, ribosomal RNA genes) usually found in lepidopteran mitogenomes. The newly sequenced mitogenome contained some common features reported in other Erebidae species, e.g., an A+T biased nucleotide composition and a non-canonical start codon for cox1 (CGA). Like other insect mitogenomes, the D. stuposa mitogenome had a conserved sequence ‘ATACTAA’ in an intergenic spacer between trnS2 and nad1, and a motif ‘ATAGA’ followed by a 20 bp poly-T stretch in the A+T rich region. Phylogenetic analyses supported D. stuposa as part of the Erebidae family and reconfirmed the monophyly of the subfamilies Arctiinae, Catocalinae and Lymantriinae within Erebidae.

scholarly journals First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera

ZooKeys ◽  
2019 ◽  
Vol 879 ◽  
pp. 137-156
Author(s):  
Mingsheng Yang ◽  
Bingyi Hu ◽  
Lin Zhou ◽  
Xiaomeng Liu ◽  
Yuxia Shi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Length Variation ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
The One ◽  
Rna Genes

The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (TψC) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.

scholarly journals Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration

2016 ◽  
Author(s):  
Fenfang Chen ◽  
Hongyu Ma ◽  
Chunyan Ma ◽  
Heng Zhang ◽  
Mengdi Zhao ◽  
...  
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Start Codon ◽  
12S Rrna ◽  
Rrna Gene ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
Rna Genes

In the present study, we isolated and characterized the complete mitochondrial genome sequence of Brama japonica by polymerase chain reaction (PCR) amplification and primer-walking sequencing. The complete DNA was 17,009 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long putative control region. The gene organization and nucleotide composition of complete mitogenome were identical to those of other Bramidae fishes. In contrast, the 12S rRNA gene contained a big poly C structure which was larger than those from other Bramidae species. Of 37 genes, twenty-eight were encoded by heavy strand, while nine were encoded by light strand. Among the 13 protein-coding genes, twelve employed ATG as start codon, while only COI utilized GTG as start codon. In the control region, the terminal associated sequence (TAS), the central and conserved sequence block (CSB-E and CSB-D) and a variable domain (CSB-1, CSB-2 and CSB-3) were identified, while the typical central conserved CSB-F could not be detected in B. japonica. The putative OL region can fold into a conserved secondary structure and the conserved motif (5’-GCCGG-3’) was found at the base of the stem in tRNACys. The overall nucleotide composition of this genome was 26.43% for A, 16.71% for G, 31.35% for C, and 25.50% for T, with a high A+T content of 51.93%. From the NJ phylogenetic tree, we can find that B. japonica was together with other five Bramidae species formed a monophyletic group among 24 species. This work provided a set of useful data for studying on population genetic diversity and molecular evolution in Bramidae and related fish species.

scholarly journals Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration

2016 ◽  
Author(s):  
Fenfang Chen ◽  
Hongyu Ma ◽  
Chunyan Ma ◽  
Heng Zhang ◽  
Mengdi Zhao ◽  
...  
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Start Codon ◽  
12S Rrna ◽  
Rrna Gene ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Protein Coding Genes ◽  
Rna Genes

In the present study, we isolated and characterized the complete mitochondrial genome sequence of Brama japonica by polymerase chain reaction (PCR) amplification and primer-walking sequencing. The complete DNA was 17,009 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long putative control region. The gene organization and nucleotide composition of complete mitogenome were identical to those of other Bramidae fishes. In contrast, the 12S rRNA gene contained a big poly C structure which was larger than those from other Bramidae species. Of 37 genes, twenty-eight were encoded by heavy strand, while nine were encoded by light strand. Among the 13 protein-coding genes, twelve employed ATG as start codon, while only COI utilized GTG as start codon. In the control region, the terminal associated sequence (TAS), the central and conserved sequence block (CSB-E and CSB-D) and a variable domain (CSB-1, CSB-2 and CSB-3) were identified, while the typical central conserved CSB-F could not be detected in B. japonica. The putative OL region can fold into a conserved secondary structure and the conserved motif (5’-GCCGG-3’) was found at the base of the stem in tRNACys. The overall nucleotide composition of this genome was 26.43% for A, 16.71% for G, 31.35% for C, and 25.50% for T, with a high A+T content of 51.93%. From the NJ phylogenetic tree, we can find that B. japonica was together with other five Bramidae species formed a monophyletic group among 24 species. This work provided a set of useful data for studying on population genetic diversity and molecular evolution in Bramidae and related fish species.

scholarly journals The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Priya Prasad ◽  
Shantanu Kundu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Gene Arrangement ◽  
Sister Relationship ◽  
Protein Coding ◽  
Relationship Of ◽  
Rna Genes ◽  
Boundary Mapping ◽  
Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

scholarly journals Characterization of the Complete Mitochondrial Genome of Fischoederius elongatus Derived from Cows in Shanghai, China

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Zhaoqing Han ◽  
Kun Li ◽  
Houqiang Luo ◽  
Muhammad Shahzad ◽  
Khalid Mehmood
Keyword(s):  
Amino Acids ◽  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Parasite Species ◽  
Codon Position ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Protein Coding ◽  
Rna Genes

A study was conducted to reveal the characterization of the complete mitochondrial genome of Fischoederius elongatus derived from cows in Shanghai, China. Results indicated that the complete mt genome of F. elongatus was 14,288 bp and contained 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6, and cytb), 22 transfer RNA genes, and two ribosomal RNA genes (l-rRNA and s-rRNA). The overall A + T content of the mt genome was 63.83%, and the nucleotide composition was A (19.83%), C (9.75%), G (26.43%), and T (44.00%). A total of 3284 amino acids were encoded by current F. elongatus isolate mt genome, TTT (Phe) (9.84%) and TTG (Leu) (7.73%) codon were the most frequent amino acids, whereas the ACC (Thr) (0.06%), GCC (Ala) (0.09%), CTC (Leu) (0.09%), and AAC (Asn) (0.09%) codon were the least frequent ones. At the third codon position of F. elongatus mt protein genes, T (50.82%) was observed most frequently and C (5.85%) was the least one. The current results can contribute to epidemiology diagnosis, molecular identification, taxonomy, genetic, and drug development researches about this parasite species in cattle.

The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽  
2019 ◽  
Vol 4671 (4) ◽  
pp. 571-580 ◽  
Author(s):  
YUE SHEN ◽  
YU-ZHOU DU
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Likelihood Methods ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Rna Genes ◽  
Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae). 

scholarly journals The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8762
Author(s):  
Yue Shen ◽  
Yu-Zhou Du
Keyword(s):  
Mitochondrial Genome ◽  
Northern Hemisphere ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Protein Coding ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

scholarly journals Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

ZooKeys ◽  
2020 ◽  
Vol 945 ◽  
pp. 1-16
Author(s):  
Yuan-An Wu ◽  
Jin-Wei Gao ◽  
Xiao-Fei Cheng ◽  
Min Xie ◽  
Xi-Ping Yuan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Amino Acid Sequences ◽  
Phylogenetic Study ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Close Relationship ◽  
Rna Genes

Azygia hwangtsiyui (Trematoda, Azygiidae), a neglected parasite of predatory fishes, is little-known in terms of its molecular epidemiology, population ecology and phylogenetic study. In the present study, the complete mitochondrial genome of A. hwangtsiyui was sequenced and characterized: it is a 13,973 bp circular DNA molecule and encodes 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as two non-coding regions. The A+T content of the A. hwangtsiyui mitogenome is 59.6% and displays a remarkable bias in nucleotide composition with a negative AT skew (–0.437) and a positive GC skew (0.408). Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family. This is the first characterization of the A. hwangtsiyui mitogenome, and the first reported mitogenome of the family Azygiidae. These novel datasets of the A. hwangtsiyui mt genome represent a meaningful resource for the development of mitochondrial markers for the identification, diagnostics, taxonomy, homology and phylogenetic relationships of trematodes.

scholarly journals The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8274 ◽  
Author(s):  
Dan Chen ◽  
Jing Liu ◽  
Luca Bartolozzi ◽  
Xia Wan
Keyword(s):  
Mitochondrial Genome ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Illumina Platform ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rna Genes ◽  
Generation Sequencing

Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

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